A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.
Report
generated on 2022-06-16, 10:58
based on data in:
/home/chengxin/pmultiqctest/test_dia/results
pmultiqc
pmultiqc is an module to show the pipeline performance.
Experimental Design
This plot shows the Proteomics Experimental Design
This plot shows the Proteomics Experimental Design. You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html
| Spectra File | Fraction_Group | Fraction | Label | Sample | MSstats_Condition | MSstats_BioReplicate |
|---|---|---|---|---|---|---|
| RD139_Narrow_UPS1_0_1fmol_inj1.mzML | 1 | 1 | 1 | 1 | CT=Mixture;CN=UPS1;QY=0.1fmol | 1 |
| RD139_Narrow_UPS1_0_1fmol_inj2.mzML | 2 | 1 | 1 | 1 | CT=Mixture;CN=UPS1;QY=0.1fmol | 1 |
| RD139_Narrow_UPS1_0_25fmol_inj1.mzML | 3 | 1 | 1 | 2 | CT=Mixture;CN=UPS1;QY=0.25fmol | 2 |
| RD139_Narrow_UPS1_0_25fmol_inj2.mzML | 4 | 1 | 1 | 2 | CT=Mixture;CN=UPS1;QY=0.25fmol | 2 |
Summary Table
This plot shows the quantms pipeline summary statistics
This plot shows the quantms pipeline summary statistics
| Total MS/MS Spectral | Total Peptide Quantified | Total Protein Quantified |
|---|---|---|
| 573300 | 5729 | 1605 |
Pipeline Result Statistics
This plot shows the quantms pipeline final result
This plot shows the quantms pipeline final result.
Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、
and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained
from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.
| Spectra File | Sample Name | condition | fraction | peptide_num | unique_peptide_num | modified_peptide_num | protein_num |
|---|---|---|---|---|---|---|---|
| RD139_Narrow_UPS1_0_1fmol_inj1.mzML | 1 | CT=Mixture;CN=UPS1;QY=0.1fmol | 1 | 5407 | 5407 | 871 | 1552 |
| RD139_Narrow_UPS1_0_1fmol_inj2.mzML | 1 | CT=Mixture;CN=UPS1;QY=0.1fmol | 1 | 5434 | 5434 | 880 | 1562 |
| RD139_Narrow_UPS1_0_25fmol_inj1.mzML | 2 | CT=Mixture;CN=UPS1;QY=0.25fmol | 1 | 5572 | 5572 | 901 | 1578 |
| RD139_Narrow_UPS1_0_25fmol_inj2.mzML | 2 | CT=Mixture;CN=UPS1;QY=0.25fmol | 1 | 5558 | 5558 | 896 | 1588 |
Number of Peptides Per Protein
This plot shows the number of peptides per proteins in quantms pipeline final result
This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.
Distribution of precursor charges
This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.
This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.
Number of Peaks per MS/MS spectrum
This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment. This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).
Peak Intensity Distribution
This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.
Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.
Peptides Quantification Table
This plot shows the quantification information of peptidesin quantms pipeline final result
The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms.
- BestSearchScore: It is equal to 1 - min(Q.Value) for DIA datasets. Then it is equal to 1 - min(best_search_engine_score[1]), which is from best_search_engine_score[1] column in mzTab peptide table for DDA datasets.
- Average Intensity: Average intensity of each peptide sequence across all conditions with NA=0 or NA ignored.
- Peptide intensity in each condition (Eg.
CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of fractions, and then mean intensity in technical replicates/biological replicates separately. Clickdistributionto switch to bar plots.
| index | ProteinName | PeptideSequence | BestSearchScore | Average Intensity | CT=Mixture;CN=UPS1;QY=0.1fmol | CT=Mixture;CN=UPS1;QY=0.25fmol | CT=Mixture;CN=UPS1;QY=0.1fmol | CT=Mixture;CN=UPS1;QY=0.25fmol |
|---|---|---|---|---|---|---|---|---|
| 1 | TOLA_ECOLI | AAAEADDIFGELSSGK | 1.00000 | 5.92624 | 5.88893 | 5.96355 | ||
| 2 | G3P2_ECOLI | AAAENIIPHTTGAAK | 0.99999 | 6.12566 | 6.08148 | 6.16983 | ||
| 3 | RLMH_ECOLI | AAAEQSWSLSALTLPHPLVR | 0.99998 | 6.23700 | 6.19528 | 6.27871 | ||
| 4 | PDXJ_ECOLI | AAAEVGAPFIEIHTGC(Carbamidomethyl)YADAK | 0.99966 | 5.38678 | 5.49758 | 5.27598 | ||
| 5 | RL10_ECOLI | AAAFEGELIPASQIDR | 1.00000 | 8.54788 | 8.50557 | 8.59019 | ||
| 6 | YFGM_ECOLI | AAAQLQQGLADTSDENLK | 1.00000 | 6.68891 | 6.69790 | 6.67992 | ||
| 7 | YFGM_ECOLI | AAAQLQQGLADTSDENLKAVINLR | 1.00000 | 6.15424 | 6.03208 | 6.27640 | ||
| 8 | RHLE_ECOLI | AAATGEALSLVC(Carbamidomethyl)VDEHK | 0.99998 | 5.70650 | 5.67986 | 5.73314 | ||
| 9 | SYP_ECOLI | AAATQEMTLVDTPNAK | 1.00000 | 6.27768 | 6.20352 | 6.35184 | ||
| 10 | EUTL_ECOLI | AAC(Carbamidomethyl)NAFTDAVLEIAR | 1.00000 | 5.62924 | 5.60437 | 5.65410 | ||
| 11 | ACRB_ECOLI | AADGQMVPFSAFSSSR | 0.99998 | 6.05977 | 5.93873 | 6.18081 | ||
| 12 | YIDA_ECOLI | AADGSTVAQTALSYDDYR | 0.99984 | 5.69853 | 5.68264 | 5.71442 | ||
| 13 | ADHE_ECOLI | AADIVLQAAIAAGAPK | 1.00000 | 7.67648 | 7.64709 | 7.70587 | ||
| 14 | NARG_ECOLI | AADLVDALGQENNPEWK | 1.00000 | 5.69054 | 5.64536 | 5.73571 | ||
| 15 | DNAK_ECOLI | AADNKSLGQFNLDGINPAPR | 0.99984 | 5.52338 | 5.49575 | 5.55101 | ||
| 16 | OXYR_ECOLI | AADSC(Carbamidomethyl)HVSQPTLSGQIR | 1.00000 | 6.58158 | 6.54958 | 6.61358 | ||
| 17 | TALA_ECOLI | AAEELEKEGINC(Carbamidomethyl)NLTLLFSFAQAR | 1.00000 | 6.26057 | 6.20589 | 6.31525 | ||
| 18 | HEMY_ECOLI | AAELAGNDTIPVEITR | 0.99995 | 6.43896 | 6.42564 | 6.45229 | ||
| 19 | SYL_ECOLI | AAENNPELAAFIDEC(Carbamidomethyl)R | 1.00000 | 6.98268 | 6.94120 | 7.02417 | ||
| 20 | TALB_ECOLI | AAEQLEKEGINC(Carbamidomethyl)NLTLLFSFAQAR | 1.00000 | 6.97373 | 6.89627 | 7.05119 | ||
| 21 | MBHM_ECOLI | AAESALNIDVPVNAQYIR | 1.00000 | 6.13352 | 6.13039 | 6.13665 | ||
| 22 | DNAG_ECOLI | AAESGVSRPVPQLKR | 0.99994 | 5.09364 | 4.95849 | 5.22879 | ||
| 23 | HDFR_ECOLI | AAESLYLTQSAVSFR | 1.00000 | 6.05307 | 6.01157 | 6.09457 | ||
| 24 | RNE_ECOLI | AAESRPAPFLIHQESNVIVR | 1.00000 | 6.57488 | 6.55722 | 6.59255 | ||
| 25 | HFLK_ECOLI | AAFDDAIAARENEQQYIR | 1.00000 | 5.77820 | 5.63543 | 5.92097 | ||
| 26 | AROF_ECOLI | AAFPLSLQQEAQIADSR | 1.00000 | 5.92732 | 5.93057 | 5.92407 | ||
| 27 | AROF_ECOLI | AAFPLSLQQEAQIADSRK | 0.99984 | 5.76026 | 5.73177 | 5.78874 | ||
| 28 | BOLA_ECOLI | AAFQPVFLEVVDESYR | 1.00000 | 6.72860 | 6.71178 | 6.74543 | ||
| 29 | CLPB_ECOLI | AAGATTANITQAIEQMR | 1.00000 | 6.06974 | 5.97263 | 6.16686 | ||
| 30 | YBIS_ECOLI | AAGEPLPAVVPAGPDNPMGLYALYIGR | 1.00000 | 5.94884 | 5.83808 | 6.05959 | ||
| 31 | SDHA_ECOLI | AAGLHLQESIAEQGALR | 1.00000 | 5.42244 | 5.42948 | 5.41540 | ||
| 32 | TALA_ECOLI | AAGLSQYEHLIDDAIAWGK | 0.99984 | 5.17878 | 5.11623 | 5.24132 | ||
| 33 | TALA_ECOLI | AAGLSQYEHLIDDAIAWGKK | 1.00000 | 5.82005 | 5.77630 | 5.86380 | ||
| 34 | ADHE_ECOLI | AAGVETEVFFEVEADPTLSIVR | 0.99999 | 6.46527 | 6.51683 | 6.41371 | ||
| 35 | ADHE_ECOLI | AAGVETEVFFEVEADPTLSIVRK | 0.99984 | 6.82885 | 6.77579 | 6.88191 | ||
| 36 | ENO_ECOLI | AAGYELGKDITLAMDC(Carbamidomethyl)AASEFYK | 1.00000 | 6.64634 | 6.62909 | 6.66359 | ||
| 37 | YEBE_ECOLI | AAHQDEPQFGAQSTPLDER | 0.99984 | 5.64827 | 5.62198 | 5.67456 | ||
| 38 | RIBB_ECOLI | AAIADGAKPSDLNRPGHVFPLR | 1.00000 | 6.46193 | 6.43130 | 6.49256 | ||
| 39 | DEOC_ECOLI | AAIAYGADEVDVVFPYR | 1.00000 | 7.04750 | 6.99277 | 7.10224 | ||
| 40 | IDH_ECOLI | AAIEYAIANDRDSVTLVHK | 1.00000 | 6.28684 | 6.26890 | 6.30479 | ||
| 41 | DPO1_ECOLI | AAINAPMQGTAADIIKR | 0.99984 | 5.87444 | 5.85167 | 5.89720 | ||
| 42 | SYFA_ECOLI | AAISQASDVAALDNVR | 1.00000 | 6.88310 | 6.87875 | 6.88744 | ||
| 43 | SYFA_ECOLI | AAISQASDVAALDNVRVEYLGK | 1.00000 | 6.04132 | 5.98363 | 6.09900 | ||
| 44 | MUKF_ECOLI | AAISSC(Carbamidomethyl)ELLLSETSGTLR | 0.99984 | 5.45034 | 5.39500 | 5.50568 | ||
| 45 | MSCM_ECOLI | AAKPAQPEVVEALQSALNALEER | 0.99993 | 5.25606 | 5.16930 | 5.34283 | ||
| 46 | AMPN_ECOLI | AALEQLKGLENLSGDLYEK | 1.00000 | 6.25426 | 6.19468 | 6.31384 | ||
| 47 | DBHA_ECOLI | AALESTLAAITESLK | 1.00000 | 7.30296 | 7.31293 | 7.29298 | ||
| 48 | HEM3_ECOLI | AALPPEISLPAVGQGAVGIEC(Carbamidomethyl)R | 0.99989 | 6.30968 | 6.27974 | 6.33962 | ||
| 49 | SDHA_ECOLI | AALQISQSGQTC(Carbamidomethyl)ALLSK | 0.99991 | 5.55626 | 5.47807 | 5.63444 | ||
| 50 | DHE4_ECOLI | AANAGGVATSGLEMAQNAAR | 1.00000 | 5.72703 | 5.66062 | 5.79344 |
Protein Quantification Table
This plot shows the quantification information of proteinsin quantms pipeline final result
The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run.
- Peptides_Number: The number of peptides for each protein.
- Average Intensity: Average intensity of each protein across all conditions with NA=0 or NA ignored.
- Protein intensity in each condition (Eg.
CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of peptides.Clickdistributionto switch to bar plots.
| ProteinName | Peptides_Number | Average Intensity | CT=Mixture;CN=UPS1;QY=0.1fmol | CT=Mixture;CN=UPS1;QY=0.25fmol | CT=Mixture;CN=UPS1;QY=0.1fmol | CT=Mixture;CN=UPS1;QY=0.25fmol |
|---|---|---|---|---|---|---|
| 3PASE_ECOLI | 1 | 5.62306 | 5.60463 | 5.64150 | ||
| 5DNU_ECOLI | 1 | 5.18693 | 5.11178 | 5.26208 | ||
| 6PGD_ECOLI | 10 | 7.42942 | 7.41428 | 7.44456 | ||
| 6PGL_ECOLI | 2 | 6.50260 | 6.47213 | 6.53307 | ||
| AAEB_ECOLI | 1 | 6.17840 | 6.14101 | 6.21578 | ||
| AAS_ECOLI | 4 | 6.06861 | 6.07277 | 6.06445 | ||
| AAT_ECOLI | 2 | 7.17292 | 7.15145 | 7.19440 | ||
| ABGT_ECOLI | 1 | 5.23376 | 5.33010 | 5.13743 | ||
| ACCA_ECOLI | 11 | 7.75792 | 7.71705 | 7.79878 | ||
| ACCC_ECOLI | 12 | 7.61524 | 7.57807 | 7.65242 | ||
| ACCD_ECOLI | 4 | 6.95665 | 6.94380 | 6.96950 | ||
| ACEA_ECOLI | 10 | 7.20604 | 7.16455 | 7.24753 | ||
| ACFD_ECOLI | 8 | 6.82809 | 6.79050 | 6.86569 | ||
| ACKA_ECOLI | 10 | 8.29284 | 8.26443 | 8.32125 | ||
| ACNA_ECOLI | 5 | 6.10554 | 6.03155 | 6.17954 | ||
| ACNB_ECOLI | 11 | 7.55688 | 7.52042 | 7.59335 | ||
| ACRA_ECOLI | 6 | 7.49514 | 7.45093 | 7.53935 | ||
| ACRB_ECOLI | 6 | 6.86423 | 6.80422 | 6.92424 | ||
| ACSA_ECOLI | 2 | 5.59331 | 5.63552 | 5.55110 | ||
| ACUI_ECOLI | 5 | 7.03398 | 6.95830 | 7.10966 | ||
| ACYP_ECOLI | 1 | 5.61388 | 5.60391 | 5.62384 | ||
| ADD_ECOLI | 5 | 7.28189 | 7.25590 | 7.30788 | ||
| ADEC_ECOLI | 1 | 5.38668 | 5.35270 | 5.42067 | ||
| ADHE_ECOLI | 36 | 8.65016 | 8.61049 | 8.68982 | ||
| ADHP_ECOLI | 2 | 6.07902 | 6.07556 | 6.08247 | ||
| ADIA_ECOLI | 3 | 5.91748 | 5.85021 | 5.98476 | ||
| ADPP_ECOLI | 2 | 6.61200 | 6.58045 | 6.64355 | ||
| AGP_ECOLI | 3 | 6.13662 | 6.10643 | 6.16680 | ||
| AHPC_ECOLI | 9 | 8.12726 | 8.09729 | 8.15722 | ||
| AHPF_ECOLI | 9 | 7.59356 | 7.57594 | 7.61117 | ||
| AHR_ECOLI | 1 | 5.05767 | 5.13523 | 4.98011 | ||
| AK1H_ECOLI | 7 | 6.48752 | 6.45929 | 6.51575 | ||
| AK2H_ECOLI | 4 | 6.50094 | 6.47209 | 6.52980 | ||
| AK3_ECOLI | 5 | 6.58938 | 6.53665 | 6.64211 | ||
| ALAA_ECOLI | 3 | 6.60599 | 6.58144 | 6.63054 | ||
| ALAC_ECOLI | 5 | 6.56726 | 6.51161 | 6.62291 | ||
| ALDB_ECOLI | 1 | 6.04168 | 6.01046 | 6.07289 | ||
| ALF1_ECOLI | 2 | 5.44720 | 5.08834 | 5.80606 | ||
| ALF_ECOLI | 10 | 8.13548 | 8.11628 | 8.15468 | ||
| ALKH_ECOLI | 3 | 6.64010 | 6.56865 | 6.71154 | ||
| ALR1_ECOLI | 3 | 6.66391 | 6.63045 | 6.69737 | ||
| AMIA_ECOLI | 1 | 5.80634 | 5.76583 | 5.84686 | ||
| AMIB_ECOLI | 2 | 5.72767 | 5.69326 | 5.76208 | ||
| AMIC_ECOLI | 5 | 5.98195 | 5.89629 | 6.06762 | ||
| AMID_ECOLI | 1 | 4.52776 | 4.35834 | 4.69717 | ||
| AMN_ECOLI | 8 | 6.76504 | 6.74232 | 6.78775 | ||
| AMPA_ECOLI | 7 | 7.26489 | 7.23293 | 7.29686 | ||
| AMPC_ECOLI | 2 | 6.11671 | 6.06209 | 6.17133 | ||
| AMPH_ECOLI | 2 | 6.15217 | 6.09222 | 6.21212 | ||
| AMPN_ECOLI | 7 | 7.10628 | 7.08197 | 7.13058 |
nf-core/quantms Software Versions
are collected at run time from the software output.
| Process Name | Software | Version |
|---|---|---|
| ASSEMBLE_EMPIRICAL_LIBRARY | DIA-NN | 1.8.1 |
| CUSTOM_DUMPSOFTWAREVERSIONS | python | 3.9.5 |
| yaml | 5.4.1 | |
| DIANNCFG | sdrf-pipelines | 0.0.21 |
| DIANNCONVERT | sdrf-pipelines | 0.0.21 |
| DIANNSUMMARY | DIA-NN | 1.8.1 |
| DIANN_PRELIMINARY_ANALYSIS | DIA-NN | 1.8.1 |
| INDIVIDUAL_FINAL_ANALYSIS | DIA-NN | 1.8.1 |
| MSSTATS | bioconductor-msstats | 4.2.0 |
| r-base | 4.1.2 | |
| SAMPLESHEET_CHECK | sdrf-pipelines | 0.0.21 |
| SDRFPARSING | sdrf-pipelines | 0.0.21 |
| THERMORAWFILEPARSER | ThermoRawFileParser | 1.3.4 |
| Workflow | Nextflow | 21.10.6 |
| nf-core/quantms | 1.1dev |
nf-core/quantms Workflow Summary
- this information is collected when the pipeline is started.
Core Nextflow options
- runName
- voluminous_thompson
- containerEngine
- docker
- launchDir
- /home/chengxin/newPR/quantms
- workDir
- /home/chengxin/newPR/quantms/work
- projectDir
- /home/chengxin/newPR/quantms
- userName
- chengxin
- profile
- test_dia,docker
- configFiles
- /home/chengxin/newPR/quantms/nextflow.config
Input/output options
- input
- /home/chengxin/diatestdata/PXD026600/PXD026600Partial2.sdrf.tsv
- outdir
- ./results_dia
Protein database
- database
- /home/chengxin/diatestdata/PXD026600/REF_EColi_K12_UPS1_combined.fasta
Database search
- allowed_missed_cleavages
- 1
- instrument
- N/A
- max_precursor_charge
- 3
- min_peptide_length
- 15
- max_peptide_length
- 30
- max_mods
- 2
Modification localization
- luciphor_debug
- N/A
PSM re-scoring (general)
- run_fdr_cutoff
- 0.10
PSM re-scoring (Percolator)
- description_correct_features
- N/A
Consensus ID
- consensusid_considered_top_hits
- N/A
- min_consensus_support
- N/A
Isobaric analyzer
- select_activation
- HCD
Protein Quantification (DDA)
- ratios
- N/A
- normalize
- N/A
- fix_peptides
- N/A
DIA-NN
- acquisition_method
- N/A
- mass_acc_ms2
- 13
- mass_acc_ms1
- 7
- scan_window
- 8
- min_pr_mz
- 350
- max_pr_mz
- 950
- min_fr_mz
- 500
- max_fr_mz
- 1500
- diann_normalize
- N/A
Statistical post-processing
- contrasts
- pairwise
Quality control
- enable_pmultiqc
- true
Institutional config options
- config_profile_name
- Test profile for DIA
- config_profile_description
- Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch.
Max job request options
- max_cpus
- 2
- max_memory
- 6 GB
- max_time
- 2d
Generic options
- hostnames
- N/A